PMC:4301621 / 33123-34014 JSONTXT

{"project":"2_test","denotations":[{"id":"25582171-20057383-14905527","span":{"begin":174,"end":176},"obj":"20057383"},{"id":"25582171-21886097-14905528","span":{"begin":327,"end":329},"obj":"21886097"},{"id":"25582171-21886097-14905529","span":{"begin":612,"end":614},"obj":"21886097"}],"text":"The reconstructed metabolic network was converted into stoichiometric matrix (S = M * N) using the Matlab program, where M represents metabolites and N represents reactions [65]. The basic tools used for model analysis were flux balance analysis (FBA) and flux variability analysis (FVA). GLPK was used for linear programming [22], and Gurobi was used for quadratic programming [66]. In silico analysis included growth simulation, gene and reaction essentiality analysis, robustness analysis, and minimization of metabolic adjustment. Analyses were performed according to the instructions for the COBRA Toolbox [22]. Constraints used in each analysis are mentioned in the results section. To analyze model parameters relevant to cell growth, the biomass equation was selected as the objective function. For analysis of ARA production, the exchange reaction of ARA was the objective function."}